User:Lindenb/Notebook/UMR915/20110628
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java api for bigwig/bigbed
svn checkout http://bigwig.googlecode.com/svn/trunk/ bigwig-read-only
cd bigwig-read-only
ant
Buildfile: build.xml
compile:
[mkdir] Created dir: /home/lindenb/src/bigwig-read-only/build
[javac] Compiling 38 source files to /home/lindenb/src/bigwig-read-only/build
[javac] Note: /home/lindenb/src/bigwig-read-only/src/org/broad/igv/bbfile/BPTree.java uses unchecked or unsafe operations.
[javac] Note: Recompile with -Xlint:unchecked for details.
dist:
[mkdir] Created dir: /home/lindenb/src/bigwig-read-only/dist
[jar] Building jar: /home/lindenb/src/bigwig-read-only/dist/BigWig.jar
BUILD SUCCESSFUL
Total time: 3 seconds
<html><script src="https://gist.github.com/1050793.js?file=BigCat.java"></script></html>
Compile
javac -cp ~/src/bigwig-read-only/dist/BigWig.jar:. BigCat.java
Exec:
java -cp /home/lindenb/src/bigwig-read-only/dist/BigWig.jar:/home/lindenb/src/bigwig-read-only/lib/log4j-1.2.15.jar:. BigCat ~/src/bigwig-read-only/test/data/chr21.bb | head chr21 9434178 9434609 chr21 9434178 9434609 chr21 9508110 9508214 chr21 9516607 9516987 chr21 9903013 9903230 chr21 9903013 9903230 chr21 9905661 9906613 chr21 9907217 9907519 chr21 9907241 9907415 chr21 9907597 9908258 $ java -cp /home/lindenb/src/bigwig-read-only/dist/BigWig.jar:/home/lindenb/src/bigwig-read-only/lib/log4j-1.2.15.jar:. BigCat -p chr21:9906000-9908000 ~/src/bigwig-read-only/test/data/chr21.bb | head chr21 9905661 9906613 chr21 9907217 9907519 chr21 9907241 9907415 chr21 9907597 9908258 $ java -cp /home/lindenb/src/bigwig-read-only/dist/BigWig.jar:/home/lindenb/src/bigwig-read-only/lib/log4j-1.2.15.jar:. BigCat -p chr21:9906000-9908000 -c ~/src/bigwig-read-only/test/data/chr21.bb | head chr21 9907217 9907519 chr21 9907241 9907415 $ java -cp /home/lindenb/src/bigwig-read-only/dist/BigWig.jar:/home/lindenb/src/bigwig-read-only/lib/log4j-1.2.15.jar:. BigCat ~/src/bigwig-read-only/test/data/wigVarStepExample.bw | head chr21 9411190 9411195 50.0 chr21 9411195 9411200 40.0 chr21 9411200 9411205 60.0 chr21 9411205 9411210 20.0 chr21 9411210 9411215 20.0 chr21 9411215 9411220 20.0 chr21 9411220 9411225 40.0 chr21 9411225 9411230 60.0 chr21 9411230 9411235 40.0 chr21 9411235 9411240 40.0 $ java -cp /home/lindenb/src/bigwig-read-only/dist/BigWig.jar:/home/lindenb/src/bigwig-read-only/lib/log4j-1.2.15.jar:. BigCat -p chr21:9906000-9908000 ~/src/bigwig-read-only/test/data/wigVarStepExample.bw | head chr21 9906000 9906005 20.0 chr21 9906005 9906010 60.0 chr21 9906010 9906015 60.0 chr21 9906015 9906020 60.0 chr21 9906020 9906025 80.0 chr21 9906025 9906030 60.0 chr21 9906030 9906035 40.0 chr21 9906035 9906040 80.0 chr21 9906040 9906045 80.0 chr21 9906045 9906050 80.0
